Nudity refers to not having any clothes on. Most species must be naked to have sexual relations. Humans and Vulcans considered nudity to be somewhat risqué and titillating. The Edo considered nudity a normal part of everyday life, however. (TNG: "Justice")
In 2266, on Planet Exo III, the android Ruk stripped Captain James T. Kirk nude and later locked him onto an android duplicator to aid Dr. Roger Korby, the long lost fiancee' of nurse Christine Chapel, to create an android duplicate of Kirk in order to take over the Enterprise to further Korby's plan to populate the universe with other androids. (TOS: "What Are Little Girls Made Of?")
Betazoid wedding ceremonies are traditionally held in complete nudity, including the participants and the guests. ("Haven", et al.)
A line in Henry V stated, "For though I speak it to you, I think the king is but a man, as I am. The violet smells to him as it doth to me, in his nakedness he appears but a man." (TNG: "The Defector")
In 2369 Captain Jean-Luc Picard was stripped of his clothes by the Cardassian Gul Madred as part of his torture and interrogation. Miles O'Brien also suffered a similar situation when he arrested by the Cardassians. (TNG: "Chain of Command, Part II", DS9: "Tribunal")
On Deep Space 9, in the weeks leading up to the Dominion War, Morn went berserk after hearing Quark's prediction of the coming doom. He hit Quark with a barstool, and ran out of his Quark's Bar and through the Promenade, screaming "We're all doomed!" He then ran into the Bajoran shrine, stark naked, and began crying to the Prophets for protection. (DS9: "Blaze of Glory")
According to the Star Trek: The Next Generation Companion, for the episode "Unnatural Selection", "the Darwin "superchildren" were originally to have appeared nude and the extras were asked to shave from the neck down. But the use of transparent furniture quickly nixed that idea, and costumes were hastily made as the extras endured stubble itch."